Method for identification of origins of replication and genes regulated by DnaA in bacteria

Olga Troyanskaya (UR '99)
Bioinformatics Program, Stanford U.
ogt@smi.stanford.edu

  

Basially, my research this year is in computational biology, a field that brings computer science and mathematics together to solve biological problems. I am mainly interested in applications of computer programming to molecular genetcs.

The first goal of my study is to compose computer programs to identify origin of DNA replication in bacterial given a complete genome. The origin is a unique site on the chromosome where DNA replication begins. The programs were written in PERL and the algorithm was based on analysis of total bacterial genomes, scoring regions for number of DnaA assembly sites, AT content, DNA adenine methylase boxes, and integration host factors (IHF) binding sites. DnaA is a protein that regulates DNA replication in bacteria, IHF regulate RNA synthesis.

Additionally, genes whose transcription could be regulated by DnaA were identified by searching for DnaA boxes preceding open reading frames. Only DnaA boxes not further than 200 bases from gene promoters were considered. A number of proteins were identified, their biological function of should be tested in cyanobacterium Synechocystis. If the approach proves to be useful, the software needs to be modified to be more user friendly, and incorporated into one large program, as opposed to separate units.

- Olga Troyanskaya (1998)

Presentations
Troyanskaya O (1999). Replication and Genes Regulated by DnaA in Bacteria. Arts and Sciences Student Symposium. University of Richmond.

Troyanskaya O, Elhai J, Salzberg S (1998). Method for identification of origins of replication and genes regulated by DnaA in bacteria. The Institute for Genomic Research (TIGR) 2nd Conference on Computational Genomics.

Troyanskaya O, Bucheimer RC, Elhai J (1998). Cloning dnaA gene from cyanobacterium Anabaena. Arts and Sciences Student Symposium. University of Richmond.

Awards
University of Richmond, Outstanding Scholar, 1999
Howard Hughes Predoctoral Fellowship, 1999
Golden Key award, 1999
Keck Summer Fellowship, 1998